This bug was in Tremulous and not with the debian package. It has long since been fixed in SVN. From the Bug report http://bugzilla.icculus.org/show_bug.cgi?id=2699 :
"Fixed in svn (when I get around to committing). In the mean time if you run into this problem again setting the cvar ui_loading to 0 should bring your cursor back." Update your client binary or do the above actions :-) This bug shouldbe closed Khalsa
